The Cenozoic evolution of SE Asia records a diverse array of tectonic processes with rifting, subduction, terrane collision and large-scale continental strike-slip faulting occurring in spatially and temporally complex relations. Oligocene seafloor spreading and rift propagation in the South China Sea are critical tectonic events that overprint an earlier phase of regional extension. Two end-member models proposed to explain the opening of the South China Sea differ in the relative importance of extrusion versus subduction as the driving mechanism. This paper treats the South China Sea region as a large multi-phase continental rift basin. Synthesizing recently published studies and using filtered Bouguer gravity data, we make a series of observations and possible interpretations to advance the notion that a hybrid tectonic models need to be proposed and tested. We present an example from the Phu Khanh Basin where flexural backstripping supports our interpretation that an ‘out-of-sequence’ rifting event was of sufficient magnitude to completely attenuate the continental crust in the ultra deep water part of the basin. The complex rift history of the region leads us to believe that future frontier hydrocarbon exploration will carry large uncertainties from basin to basin.